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Greenwold MJ, Merritt K, Richardson TL, Dudycha JL. A three-genome ultraconserved element phylogeny of cryptophytes. Protist 2023; 174:125994. [PMID: 37935085 DOI: 10.1016/j.protis.2023.125994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/18/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023]
Abstract
Cryptophytes are single celled protists found in all aquatic environments. They are composed of a heterotrophic genus, Goniomonas, and a largely autotrophic group comprising many genera. Cryptophytes evolved through secondary endosymbiosis between a host eukaryotic heterotroph and a symbiont red alga. This merger resulted in a four-genome system that includes the nuclear and mitochondrial genomes from the host and a second nuclear genome (nucleomorph) and plastid genome inherited from the symbiont. Here, we make use of different genomes (with potentially distinct evolutionary histories) to perform a phylogenomic study of the early history of cryptophytes. Using ultraconserved elements from the host nuclear genome and symbiont nucleomorph and plastid genomes, we produce a three-genome phylogeny of 91 strains of cryptophytes. Our phylogenetic analyses find that that there are three major cryptophyte clades: Clade 1 comprises Chroomonas and Hemiselmis species, Clade 2, a taxonomically rich clade, comprises at least twelve genera, and Clade 3, comprises the heterotrophic Goniomonas species. Each of these major clades include both freshwater and marine species, but subclades within these clades differ in degrees of niche conservatism. Finally, we discuss priorities for taxonomic revision to Cryptophyceae based on previous studies and in light of these phylogenomic analyses.
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Affiliation(s)
- Matthew J Greenwold
- Biology Department, University of Texas at Tyler, 3900 University Blvd., Tyler, TX, 75799, USA.
| | - Kristiaän Merritt
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC 29208, USA
| | - Tammi L Richardson
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC 29208, USA; School of the Earth, Ocean, and Environment, University of South Carolina, 715 Sumter St., Columbia, SC 29208, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC 29208, USA
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2
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Korotkova DD, Lyubetsky VA, Ivanova AS, Rubanov LI, Seliverstov AV, Zverkov OA, Martynova NY, Nesterenko AM, Tereshina MB, Peshkin L, Zaraisky AG. Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration. Cell Rep 2020; 29:1027-1040.e6. [PMID: 31644900 PMCID: PMC6871517 DOI: 10.1016/j.celrep.2019.09.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/28/2019] [Accepted: 09/13/2019] [Indexed: 01/28/2023] Open
Abstract
The molecular basis of higher regenerative capacity of cold-blooded animals comparing to warm-blooded ones is poorly understood. Although this difference in regenerative capacities is commonly thought to be a result of restructuring of the same regulatory gene network, we hypothesized that it may be due to loss of some genes essential for regeneration. We describe here a bioinformatic method that allowed us to identify such genes. For investigation in depth we selected one of them encoding transmembrane protein, named “c-Answer.” Using the Xenopus laevis frog as a model cold-blooded animal, we established that c-Answer regulates regeneration of body appendages and telencephalic development through binding to fibroblast growth factor receptors (FGFRs) and P2ry1 receptors and promoting MAPK/ERK and purinergic signaling. This suggests that elimination of c-answer in warm-blooded animals could lead to decreased activity of at least two signaling pathways, which in turn might contribute to changes in mechanisms regulating regeneration and telencephalic development.
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Affiliation(s)
- Daria D Korotkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Vassily A Lyubetsky
- The Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), 19 Bolshoy Karetny str., Moscow 127051, Russia
| | - Anastasia S Ivanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Lev I Rubanov
- The Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), 19 Bolshoy Karetny str., Moscow 127051, Russia
| | - Alexander V Seliverstov
- The Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), 19 Bolshoy Karetny str., Moscow 127051, Russia
| | - Oleg A Zverkov
- The Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), 19 Bolshoy Karetny str., Moscow 127051, Russia
| | - Natalia Yu Martynova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Alexey M Nesterenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, Moscow 119991, Russia
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya str., Moscow 117997, Russia.
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Zverkov OA, Mikhailov KV, Isaev SV, Rusin LY, Popova OV, Logacheva MD, Penin AA, Moroz LL, Panchin YV, Lyubetsky VA, Aleoshin VV. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Front Genet 2019; 10:443. [PMID: 31178892 PMCID: PMC6543705 DOI: 10.3389/fgene.2019.00443] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 04/29/2019] [Indexed: 01/22/2023] Open
Abstract
Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.
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Affiliation(s)
- Oleg A. Zverkov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Kirill V. Mikhailov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V. Isaev
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid Y. Rusin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V. Popova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey A. Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid L. Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Yuri V. Panchin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vassily A. Lyubetsky
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V. Aleoshin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Le TS, Yang FJ, Lo YH, Chang TC, Hsu JC, Kao CY, Wang J. Non-Mendelian assortment of homologous autosomes of different sizes in males is the ancestral state in the Caenorhabditis lineage. Sci Rep 2017; 7:12819. [PMID: 28993668 PMCID: PMC5634442 DOI: 10.1038/s41598-017-13215-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/19/2017] [Indexed: 01/25/2023] Open
Abstract
Organismal genome sizes vary by six orders of magnitude and appear positively correlated with organismal size and complexity. Neutral models have been proposed to explain the broad patterns of genome size variation based on organism population sizes. In the Caenorhabditis genus, hermaphrodite genomes are smaller than those of gonochoristic species. One possible driving force for this genome size difference could be non-random chromosome segregation. In Caenorhabditis elegans, chromosome assortment is non-independent and violates Mendel's second law. In males, the shorter homologue of a heterozygous autosome pair preferentially co-segregates with the X chromosome while the longer one preferentially co-segregates with the nullo-X (O) chromosome in a process we call "skew". Since hermaphrodites preferentially receive the shorter chromosomes and can start populations independently, their genome size would be predicted to decrease over evolutionary time. If skew is an important driver for genome size reduction in hermaphroditic Caenorhabditis species, then it should be present in all congeneric species. In this study, we tested this hypothesis and found that skew is present in all eight examined species. Our results suggest that skew is likely the ancestral state in this genus. More speculatively, skew may drive genome size patterns in hermaphroditic species in other nematodes.
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Affiliation(s)
- Tho Son Le
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.,Department of Molecular Genetics and Gene Technology, College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Fang-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Hua Lo
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tiffany C Chang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Jung-Chen Hsu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Yi Kao
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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Gershgorin RA, Gorbunov KY, Zverkov OA, Rubanov LI, Seliverstov AV, Lyubetsky VA. Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates. Life (Basel) 2017; 7:E9. [PMID: 28264444 PMCID: PMC5370409 DOI: 10.3390/life7010009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 11/30/2022] Open
Abstract
Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome.
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Affiliation(s)
- Roman A Gershgorin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Konstantin Yu Gorbunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Oleg A Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Lev I Rubanov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Alexandr V Seliverstov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskiye Gory 1, Main Building, Moscow 119991, Russia.
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Molecular Phylogenetics 2016. BIOMED RESEARCH INTERNATIONAL 2017; 2016:9029306. [PMID: 28127550 PMCID: PMC5227124 DOI: 10.1155/2016/9029306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 11/17/2022]
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